VNtyper 2.0 is an advanced pipeline designed to genotype MUC1 coding Variable Number Tandem Repeats (VNTR) in Autosomal Dominant Tubulointerstitial Kidney Disease (ADTKD-MUC1) using Short-Read Sequencing (SRS) data. This version integrates enhanced variant calling algorithms, robust logging mechanisms, and streamlined installation processes to provide researchers with a powerful tool for VNTR analysis.
Variant Calling Algorithms:
Comprehensive Logging:
Flexible Installation:
pip
using setup.py
.Subcommands:
install-references
pipeline
fastq
bam
kestrel
report
cohort
VNtyper 2.0 can be installed using either pip
with setup.py
or via Conda environments for streamlined dependency management.
setup.py
and pip
Clone the Repository:
mkdir vntyper
git clone https://github.com/hassansaei/vntyper.git
cd vntyper
pip install .
VNtyper 2.0 offers multiple subcommands that can be used depending on your input data and requirements. Below are the main subcommands available:
To run the entire pipeline on paired-end FASTQ files or BAM files:
vntyper pipeline \
--config-path /path/to/config.json \
--fastq1 /path/to/sample_R1.fastq.gz \
--fastq2 /path/to/sample_R2.fastq.gz \
--output-dir /path/to/output/dir \
--threads 4
Alternatively, using a BAM file:
vntyper pipeline \
--config-path /path/to/config.json \
--bam /path/to/sample.bam \
--output-dir /path/to/output/dir \
--threads 4
vntyper install-references \
--output-dir /path/to/reference/install \
--config-path /path/to/config.json \
--skip-indexing # Optional: skip BWA indexing if needed
Generate a summary report for your VNTR genotyping analysis:
vntyper report \
--output-dir /path/to/output/dir \
--config-path /path/to/config.json
Process raw FASTQ files to prepare them for genotyping:
vntyper fastq \
--fastq1 /path/to/sample_R1.fastq.gz \
--fastq2 /path/to/sample_R2.fastq.gz \
--output-dir /path/to/output/dir
vntyper bam \
--alignment /path/to/sample.bam \
--output-dir /path/to/output/dir \
--threads 4
VNtyper 2.0 integrates multiple steps into a streamlined pipeline. The following is an overview of the steps involved:
VNtyper 2.0 relies on several tools and Python libraries. Ensure that the following dependencies are available in your environment:
You can easily set up these dependencies via the provided Conda environment file.
Below is a logical overview of the VNtyper pipeline:
graph TD
A[Input: FASTQ/BAM] -->|Quality Control| B[Alignment BWA]
B -->|Genotyping| C[Kestrel]
C --> D[Optional: adVNTR]
D --> E[Generate Summary Report]
E --> F[Output: VCF, Summary HTML]
If you use VNtyper 2.0 in your research, please cite the following:
We welcome contributions to VNtyper. Please refer to the CONTRIBUTING.md file for guidelines.
VNtyper is licensed under the BSD 3-Clause License. See the LICENSE file for more details.